GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Pseudomonas fluorescens GW456-L13

Align amino-acid N-acetyltransferase (EC 2.3.1.1) (characterized)
to candidate PfGW456L13_3289 Protein export cytoplasm protein SecA ATPase RNA helicase (TC 3.A.5.1.1)

Query= BRENDA::Q9I3W7
         (177 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3289
          Length = 173

 Score =  233 bits (595), Expect = 1e-66
 Identities = 117/170 (68%), Positives = 136/170 (80%), Gaps = 2/170 (1%)

Query: 1   MTAESPTIRLERYSERHVEGLTALYNDPAVARQVLQMPYQSVEQRRKRLHDSADDDRLLI 60
           M A  P I LER++E H+EG+ ALYNDPA+ARQ LQMP+QS E  R RL  + D++RL+ 
Sbjct: 1   MPATEPVITLERFNESHIEGVAALYNDPAIARQTLQMPFQSTELWRSRL--ALDNERLVN 58

Query: 61  LVALHQGDVIGSASLEQHPRIRRSHSGSIGMGVAVAWQGKGVGSRLLGELLDIADNWMNL 120
           +VALHQG VIG+  LEQ  RIRRSH+GS GMGVAVAWQGKGVGS+LL   LDIADNWMNL
Sbjct: 59  VVALHQGTVIGNIGLEQFSRIRRSHAGSFGMGVAVAWQGKGVGSKLLATALDIADNWMNL 118

Query: 121 RRVELTVYTDNAPALALYRKFGFETEGEMRDYAVRDGRFVDVYSMARLRR 170
           +R+EL+VY DN  A++LYRKFGFETEG  RDYAVRDG  VD  SMARLRR
Sbjct: 119 QRIELSVYADNEAAISLYRKFGFETEGLFRDYAVRDGVLVDTLSMARLRR 168


Lambda     K      H
   0.320    0.136    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 162
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 177
Length of database: 173
Length adjustment: 19
Effective length of query: 158
Effective length of database: 154
Effective search space:    24332
Effective search space used:    24332
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 44 (21.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory